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Hundreds of sex offenders released on parole have been permitted to remain free even though they were arrested for new crimes over the past year, state prison officials say.

Terri McDonald, undersecretary of the state Department of Corrections and Rehabilitation, said that more than 4,000 sex offenders were sent back to jail after committing new crimes since Oct. 1, 2011, when the state launched a program to shift tens of thousands of inmates from state prisons to county jails.

But 481 sex offenders were arrested 862 times over the same period, and all of them avoided lockup, she said.

“What we have is a small number of cases and a small number of counties at a small number of times where the jail capacity is such that some offenders are not returned to custody,” McDonald said. “There have been challenges associated with this.”

The information came to light after The Watchdog requested details about how prison officials are managing realignment, the 2011 legislation that steered tens of thousands of state inmates to county jails.

Monitoring sexual predators is a particularly sensitive topic in San Diego County because registered sex offender John Gardner violated parole repeatedly without being sent back to prison and then killed two North County teenagers.

Gardner pleaded guilty in 2010 to murdering Amber Dubois and Chelsea King and is now serving life in prison.

It is unclear how many of the convicts committed fresh offenses in San Diego County. The corrections department would not say, and county officials say most parolees under their watch who break new laws are shipped back to jail.

Statewide, the failure to lock up nearly 500 rapists, child molesters and other convicts has angered rank-and-file parole agents and raised questions about California’s year-old experiment in “realignment,” as the program is known.

One parole agent has complained to the California State Auditor anonymously, saying he speaks for others and demanding an investigation of the state’s handling of sex offenders. He claims at least 150 of them have cut off their electronic monitoring bracelets, loiter near parks or schools or live with children in violation of parole conditions because they know there will be no consequences.

“One recently in Fresno was arrested and released six times before he was finally rearrested for annoying/molesting a child,” the agent wrote. “We can no longer remain silent.”

A spokeswoman for State Auditor Elaine Howle said the office does not comment on complaints or open investigations.

Agents are reluctant to speak publicly because they fear they will be retaliated against by supervisors. Retired agents are not so shy about questioning the program.

“Committed, dedicated departmental employees are deeply wounded by their inability to work to enhance public safety,” longtime agent Robert Walsh said. Prison officials “are moving to dump huge numbers of parolees out of the system in order to save the cost of supervising them, regardless of the public-safety impact.”